[gmx-users] two chains

[özge kül]

Hi 
   
  Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain?Are the parameters must be different ?Also I want to ask about trajconv.Where I had to add the pbc?I want to send you my directions.
  1.      pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o  1ppbfree.gro   
  2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
  3.      genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
  4.      grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top
  5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr
   
  or is the pbc used in the script?
  Thank You very much....
  Özge
   

 
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